R/mockPhenotypeR.R

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

#' Function to create a mock cdm reference for mockPhenotypeR
#'
#' @description
#' `mockPhenotypeR()` creates an example dataset that can be used to show how
#' the package works
#'
#' @param nPerson number of people in the cdm.
#' @param con  A DBI connection to create the cdm mock object.
#' @param writeSchema Name of an schema on the same connection with writing
#' permissions.
#' @param seed seed to use when creating the mock data.
#'
#' @return cdm object
#' @export
#'
#' @examples
#' \donttest{
#' library(PhenotypeR)
#'
#' cdm <- mockPhenotypeR()
#'
#' cdm
#' }
mockPhenotypeR <- function(nPerson = 100,
                           con = DBI::dbConnect(duckdb::duckdb()),
                           writeSchema = "main",
                           seed = 111){

  omopgenerics::assertNumeric(nPerson, length = 1, na = FALSE, null = FALSE)
  omopgenerics::assertNumeric(seed, length = 1, na = FALSE, null = FALSE)
  omopgenerics::assertCharacter(writeSchema, length = 1, na = FALSE, null = FALSE)

  cdm_local <- omock::mockCdmReference() |>
    omock::mockPerson(nPerson = 100, seed = seed) |>
    omock::mockObservationPeriod(seed = seed) |>
    omock::mockConditionOccurrence(seed = seed) |>
    omock::mockVisitOccurrence(seed = seed) |>
    omock::mockDrugExposure(seed = seed) |>
    omock::mockObservation(seed = seed) |>
    omock::mockMeasurement(seed = seed) |>
    omock::mockProcedureOccurrence(seed = seed) |>
    omock::mockCohort(name = "my_cohort", numberCohorts = 2)

  cdm <- CDMConnector::copyCdmTo(con = con,
                                   cdm = cdm_local,
                                   schema = writeSchema,
                                   overwrite = TRUE)
  attr(cdm, "write_schema") <- writeSchema

  return(cdm)
}